Hello,

I've been working with hugene20sttranscriptcluster.db_2.14.0 (most recent release version) for the last couple of days, and noticed that some of our usual marker genes appear to not be present in the annotation package. These genes are present in current and previous versions of the Affymetrix probe -> gene mappings from NETAFFX.
For example, transcript cluster 16966809 should correspond to gene symbol PDGFRA and Entrez ID 5156 (which is included in the NA34 annotation release for the platform) but any(mappedkeys(hugene20sttranscriptclusterSYMBOL) == "16966809") turns up FALSE. Picking a random transcript cluster, 16748695 (PDE6H), turns up TRUE and will return the symbol. I'm not sure if there are other genes missing as well, since I happened to stumble across this one.

For now I can try to build an annotation database from the affy annotation. Am I missing something or can someone else confirm that things are missing?

Quick copy-paste example:
library(hugene20sttranscriptcluster.db, annotate)
any(mappedkeys(hugene20sttranscriptclusterSYMBOL) == "16966809")


> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hugene20sttranscriptcluster.db_2.14.0 OrderedList_1.36.0                    twilight_1.40.0                       BiocInstaller_1.14.2
 [5] doParallel_1.0.8                      iterators_1.0.7                       limma_3.20.4                          gplots_2.13.0
 [9] xlsx_0.5.5                            xlsxjars_0.6.0                        rJava_0.9-6                           annotate_1.42.0
[13] SCAN.UPC_2.6.0                        sva_3.10.0                            mgcv_1.7-29                           nlme_3.1-117
[17] corpcor_1.6.6                         foreach_1.4.2                         affyio_1.32.0                         affy_1.42.2
[21] GEOquery_2.30.0                       oligo_1.28.2                          Biostrings_2.32.0                     XVector_0.4.0
[25] IRanges_1.22.7                        oligoClasses_1.26.0                   org.Hs.eg.db_2.14.0                   RSQLite_0.11.4
[29] DBI_0.2-7                             AnnotationDbi_1.26.0                  GenomeInfoDb_1.0.2                    Biobase_2.24.0
[33] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] affxparser_1.36.0     bit_1.1-12            bitops_1.0-6          caTools_1.17          codetools_0.2-8       ff_2.2-13             gdata_2.13.3
 [8] GenomicRanges_1.16.3  grid_3.1.0            gtools_3.4.0          KernSmooth_2.23-12    lattice_0.20-29       MASS_7.3-31           Matrix_1.1-3
[15] preprocessCore_1.26.1 RCurl_1.95-4.1        stats4_3.1.0          tools_3.1.0           XML_3.98-1.1          xtable_1.7-3          zlibbioc_1.10.0


Adam Cornwell
Programmer/Analyst


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